BIOC13 Flashcards - Citric Acid Cycle (Nhien)

Question 1

What role does the TCA cycle play?

Answer 1

A central role.
Its a cycle.

Its highly interconnected

Question 2

What can enter the TCA cycle as Acetyl CoA?

Answer 2

Fats: fatty acids and glycerol

Polysaccharides: glucose and other sugars

Proteins: amino acids

Question 3

Importance of the TCA cycle (3 points)

Answer 3

1. Its central to aerobic metabolism and ATP production, generating the bulk of NADH and FADH2, which is going to be oxidized later to generate ATP
2. Links the oxidation of metabolic fuels to ATP synthesis (fatty acids, amino acids, carbohydrates can be oxidized to Acetyl coA)
3. Provides metabolic intermediates for several biosyntehtic pathways (thats why you need to run the TCA cycle even if you dont need energy)

Question 4

Coenzyme A is the activated carrier of

Answer 4

Acetyl groups (2C)

Question 5

CoEnzyme A is also known as

Answer 5

CoASH

Question 6

What are the 2 substrates needed to start the TCA cycle

Answer 6

• Oxaloacetate (4C) generated by pyruvate carboxylase. will be regenerated after 1 run of the cycle
• Acetyl CoA (2C), generated from pyruvate dehydrogenase complex (PDH), fatty acid degradation, amino acid breakdown.

-> Pyruvate is used to syntheisze Acetyl coA and OAA.
Pyruvate needs to be transported from the cytosol (glycolysis/gluconeogenesis) into the mitochondrial matix

Question 7

How is pyruvate transported inside the mitochondria? What are the 2 fates of pyruvate after this

Answer 7

Transported via mitochondrial pyruvate carrier (MPC).

2 fates:
Inside the mitochondria, pyruvate can be used by pyruvate carboxylase -> OAA and pyruvate dehydrogenase -> Acetyl coA

Question 8

How would a 100% lipids diet affect the TCA cycle?

Answer 8

Acetyl coA can be gained from amino acids, fatty acids, glyrols, carbohydrates. (oxidation of these molecules)

But you still need OAA, which comes from pyruvate -> need carbs

Question 9

What will be the substrates of TCA, starting with Glucose

Answer 9

Glucose -> pyruvate -> 2 ways into Acetyl coA or Oxaloacetate

Question 10

What will be the substrates of TCA, starting with fatty acids

Answer 10

fatty acids -> acetyl coA.

Pyruvate -> OAA

cycle stats

Question 11

What is the pyruvate dehydrogenase complex?

Answer 11

A mitochondrial matrix enzyme, which OXIDATIVELY DECARBOXYLATES pyruvate to form acetyl coA

Question 12

What is PDH made of

Answer 12

3 enzymes: 2 dehydrogenases and 1 transcetylase

Question 13

Being part of a complex facilitates substrate channeling. What does substrate channeling do.

Answer 13

It allows substrates to travel from 1 active site to another with the help of the lipoamide arm (LD)

Question 14

What is the overall reaction of the PHD? Is this irreversible?

Answer 14

irreversible reaction: Pyruvate + CoA + NAD+ -> Acetyl CoA + Co2 + NADH + H+

Question 15

What are cofactors?

Answer 15

Some enzymes require the addition of another non-protein molecule to function as an enzyme

Question 16

What are the cofactors of PDH?

Answer 16

LD: lipoamide domain

TPP: thiamine pyrophosphate

FAD: flavin adenine dinucleotide

Question 17

Explain the 3 reactions of PDH

Answer 17

1. E1. Decarboxylation of pyruvate, carried out by pyruvate dehydrogenase
   TPP acts as cofactor to extract the Co2

Lipoamide arm carries the 1st hydrogen

2. Transfer actyl group to coA with the help of cofactor: lipamide arm

enzyme: dihydrolipoyl transecetylase

lipoamide arm carries 2nd hydrogen

3. Regeneration of oxidized lipoamide with the help of cofactor FAD.

like it loads electrons/protons onto FADH2 -> reduced to NADH
-> oxidized to NAD+
Generates NADH

Enzyme: dihydrolipoyl dehydrogenase

Question 18

What does the PDH complex look like

Answer 18

E2 in the center with lioamide arms, carry substrate from active site to active site.

Increases overall reaction rate and minimizes side reactions

Question 19

Purpose of enzyme cofactors/coenzymes

Answer 19

Expand the repertoire of reactions

Question 20

Purpose of cofactors in PDH

Answer 20

TPP: extract Co2 from pyruvate

Lipoamide: hold tightly to acetyle groups and transfer them

FAD: restore lipoamide

Humans cannot make these cofactors -> need to take vitamins

Question 21

Why must steps in PDH be coupled

Answer 21

Steps must be coupled to preserve the free energy derived from the decarboxylation to drive NADH and acetyl CoA formation

Question 22

What is the rate limiitng step of the PDH

Answer 22

(E1) Pyruvate dehydrogenase and TPP:
decarboxylation of pyruvate

Question 23

Step by step sequence of reactions of PDH.

Answer 23

1. Pyruvate is decarboxylated to from hydroxyethyl-TPP by E1, releasing Co2 as the first product.

Enzyme: pyruvate decarboxylase

2. The lipoamide arm of E2 moves into the active site of E1
3. E1 catalyzes the transfer of the 2 carbon group to the lipoamide group, forming the acetyl-lipoamide complex, enters E2.

Lipoamide arm is reduced: 1 SH

4. E2 catalyzes the transfer of the acetyl moiety to form product Acetyl- CoA. the lipoamide arm then swings to active site of E3.

ENzyme: dihydroli transetelase

5. E3 catalyzes the oxidation of the lipoamide arm by FAD

Enzyme: dihydroli dehydrogenase

6. The final product NADH is produced by the reoxidation of FADH2

Question 24

is the conversion of pyruvate to Acetyl CoA irreversible

Answer 24

yes. once pyrvuate is turned into acetyl CoA, can no longer be converted into glucose (in humans)

Question 25

What fates does Acetyl coA have? How is it regulated

Answer 25

Acetyl coA has 2 main fates: 1. Metabolism by the citric acid cycle 2. incorporation into fatty acids Regulated by 2 mechanisms. 1. Allosteric regulators 2. covalent modifications (phosphorylation)

Question 26

Is feedback inhibition a form of allosteric regulation?

Answer 26

Yes. The end product binding to the allosteric site delays or prevents the enzyme's activity, resulting in slight or no further end product being produced.

Question 27

How is PDH regulated allosterically? (-) and (+)

Answer 27

(-) ATP Acetyl coA, NADH: feedback inhibtion Increase in Acetyl CoA -> inhibits E2 (transacetulase) -> no need to metabolize pyruvate to acetyl coA. Increase in NADH -> inhbits E3 (dehydrogenase) -> no need to metabolize pyruvate to acetyl coA (+) Pyruvate: more substrate -> make more

Question 28

How is PDh regulated by covalent modication

Answer 28

E1 of PDH can be phosphorylated -> inactivates E1 Not phosphorylated -> remains active PDH kinase is active -> phosphorylates E1 -> inactivates E1 PDH phosphatase is active -> dephosphorylates E1 -> activates E1

Question 29

How is the phosphorylation of E1 regulated

Answer 29

For the kinase: (+) ATP, NADH -> phosphrylates E1 -> promotes the activity of kinase -> PDH is inactive -> cells have enough energy (-) ADP, pyruvate -> inhibits phosphrylation of E1 -> decreases activity of kinase -> E1 is dephsophrylated -> PDH is active For the phosphatase Insulin -> promotes activity of phosphatase -> dephosphorylate -> makes PDH active -> cause there glucose (espcially after eating), you should break it down. (+) Calcium muscles exert energy -> calcium increases -> stimulates the dephosphorylation -> PDH active -> obtain energy from TCa cycle

Question 30

Insulin activates/deactivates phosphatase

Answer 30

Activates

Question 31

Effect of insulin on the synthesis of Acetyl CoA

Answer 31

Insulin promotes the synthesis of Acetyl CoA

Question 32

Regulators of PDH, PDH kinase (PDH off), PDH phosphatase)

Answer 32

PDH: (-) ATP, NADH (+) Pyruvate PDH kinase: (+) ATP, NADH (-) ADP, Pyruvate PDH phosphatase: (+) Ca2+, insulin

Question 33

Ca2+ stimulates phosphatase/kinase

Answer 33

Phosphatase

Question 34

When you are at rest, that state is referred to as, when you are exercising, that state is referred to as:

Answer 34

at rest: high energy during exerise: low energy

Question 35

When you are at rest, what ratios are high? What affects the PDH

Answer 35

High ATP/ADP, NADH/NAD, Acetyl CoA/CoA ATP (-) E1 (because it promotes kiinase phosphorylation -> inactivates PDH Acetyl coA (-) E2 NADH (-) E3 (feedback inhibition) -> no need to run TCA cycle

Question 36

When you are exercising, what ratios are low? What affects the PDH?

Answer 36

Low NADH/NAD+, Acetyl CoA/CoA, ATP/ADP ADP -> reduces kinase activity -> kinase does not phosphorylate PDH -> activates PDH (E1) Calcium stimulates phosphatase. Removes phosphate group from PDH. PDH is on when energy charge is low. Pyruvate (+) PDH -> need to run TCA to obtain energy

Question 37

How does PDH link glycolysis and the TCA cycle?

Answer 37

By forming acetyl coA from pyruvate

Question 38

The fates of pyruvate and reciprocal regulation

Answer 38

Acetyl CoA controls both pyruvate carboxylase and pyruvate dehydrogenase Acetyl coA feedback inhibits pyruvate dehyogenase Acetyl coA (+) pyruvate carboxylase (indicates more OAA is needed to start TCA)

Question 39

Pyruvate is an intermediate for glucose oxdiation and precursor for..

Answer 39

the synthesis of glucose, glycerol, fatty acids and amino acisd

Question 40

Explain the increase in pyruvate and lactate, defect in muscle activity when PDH is affected

Answer 40

lack of PDH -> build up of pyruvate -> build up of lactate since pyruvate undergoes lactic fermentatin -> lack of energy -> muscles affectsed

Question 41

Treatmnets for PDH deficiency

Answer 41

keto diet

Question 42

In diabetic patients, there is an increase/decrease in PDH kinase activity

Answer 42

increase -> target the inhibition of kinase